From 5dc1f7d7307baea519b37b4aa0e0e12dce284e17 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Mon, 6 May 2024 17:11:54 -0400 Subject: [PATCH] Use correct target score for having full length bonus --- test/t/50_vg_giraffe.t | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/t/50_vg_giraffe.t b/test/t/50_vg_giraffe.t index 639f17c58d8..66e1ac75f9e 100644 --- a/test/t/50_vg_giraffe.t +++ b/test/t/50_vg_giraffe.t @@ -212,7 +212,7 @@ vg index -j 1mb1kgp.dist 1mb1kgp.vg vg autoindex -p 1mb1kgp -w giraffe -P "VG w/ Variant Paths:1mb1kgp.vg" -P "Giraffe Distance Index:1mb1kgp.dist" -r 1mb1kgp/z.fa -v 1mb1kgp/z.vcf.gz vg giraffe -Z 1mb1kgp.giraffe.gbz -f reads/1mb1kgp_longread.fq >longread.gam -U 300 --progress --track-provenance --align-from-chains # This is an 8001 bp read with 1 insert and 1 substitution -is "$(vg view -aj longread.gam | jq -r '.score')" "7989" "A long read can be correctly aligned" +is "$(vg view -aj longread.gam | jq -r '.score')" "7999" "A long read can be correctly aligned" is "$(vg view -aj longread.gam | jq -c '.path.mapping[].edit[] | select(.sequence)' | wc -l)" "2" "A long read has the correct edits found" is "$(vg view -aj longread.gam | jq -c '. | select(.annotation["filter_3_cluster-coverage_cluster_passed_size_total"] <= 300)' | wc -l)" "1" "Long read minimizer set is correctly restricted"